Data associated with paper “The GENCODE pseudogene resource”

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Q:
Your work on the ENCODE project has helped to
produce an incredible set of data!

I had a question about your pseudogene article, "The GENCODE
pseudogene resource." You note that at least 9% of them are
transcribed. Do you have a list somewhere? I couldn’t find a
supplementary file that might contain such a list. I realize it would
be quite long, but I assume it must exist somewhere. If not, do you
happen to know if the GULO pseudogene is one of the transcribed
pseudogenes?

A:
It transcribes pseudogenes should be available from the resource associated with the paper.

The data associated with the paper is located at http://pseudogene.org/psidr/

Data associated with paper “Redefining Nodes and Edges: Relating 3D Structures to Protein Networks Provides Insight into their Evolution”

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Q:

I’m hoping to analyse the data from your 2006 "Redefining Nodes and Edges: Relating 3D Structures to Protein Networks Provides Insight into their Evolution" paper. Do you have the full dataset including the pdb ids/chain ids relating to each interaction in the network?

A:
have you seen assoc. paper website : http://papers.gersteinlab.org/papers/structint

Data associated with paper “Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data”

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Q:
Hello. I read your article in PLoS Computational Biology titled "Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data". It is very interesting and nice study. I really love it!!

Would it be possible to obtain your data and networks that you have used in this article? I would like to add our own data to expand the networks.

I apologize for this sudden request, but I really would like to work with your networks.

Thank you very much for your time. I am looking forward to hearing from you soon.

A:
check out modencode.org where you can download different versions of the networks.

In additional to the link sent by Mark, which provides the most
updated raw data we are using, you can also find processed regulatory
interactions here: http://archive.gersteinlab.org/proj/mirnet/

Since the data is keep being updated, the new data from modENCODE
website might be slightly different from the one used in the paper.

subway network maps

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Q:

I’ve really enjoyed seeing your subway network maps. Our institute at Duke has an external review coming up, and I was wondering if any of the code you’ve developed might be applicable to visualize the published interactions within our institute as well as outside with other investigators across the Duke campus.

Thoughts, or is this still too early?

And I bet I’m not the only one who would be interested in this. Are you planning to publish this method? I would think many universities/groups would find this informative to understand where the interactions are happening across campus and where they aren’t happening enough.

A:
I am very enthusiastic that you find our analysis of publication
networks interesting. We just sent out a more extensive description
of this to the analysis group.

In relation to the software, we actually constructed a package for
doing literature networks and distributed some software associated
with it. It is called PubNet and it is available at
pubnet.gersteinlab.org. Unfortunately the web server does not work
that well as of late, mostly due to changes in the NCBI’s PubMed
system, but you can still download the software and do the queries
manually if you want to. I hope this is of use.

Question about paper Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

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Q:

I am very interested in Chao Cheng’s paper Construction and Analysis of an Integrated Regulatory Network
Derived from High-Throughput Sequencing Data. It is great resource for me to
analysis regulation network of C elegans.

However, I met troubles in downloading the Table S2 and Table S3 from
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190#cor1.
Is it possible to send me the supporting tables by email?

A:
Thanks for your interest in our work. Please find the tables in the attached files. Let me know if you need more information.

TableS2.xls

TableS3.xls

pseudogenes in bacteria

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Q:

I see you have developed pipelines to look for pseudogenes. Is there someone still working on this problem in your lab?

It turns out there is no good method to find pseudogenes in bacteria, which is perhaps a less challenging problem than in eukaryotes, because of the lack of splicing. There is a real need for such a pipeline because genome degradation is a common pathway to specialization in pathogens. We have hundreds of genomes we would like to put through such a pipeline.

A:
turns out we’ve done pgenes in bacteria and have some old lists available. See :
http://papers.gersteinlab.org/papers/prok-pgenes

Cavity.exe within 3V

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Q1:

I am using your program 3V for computing the volume of the active site
of a protein which is clearly external. I am using your program Cavity.exe of
3V. However, I do not know how to interpret the results of the run. It
would be nice if you please help me on this regards,

A1:
If the site is external then you are probably looking for a channel
rather than a cavity. Cavities are completely enclosed by the structure.
My suggestion would be to use the AllChannel.exe program and play with
the probe sizes.

The output from can be in several forms, but I typically use the -m
volume.mrc, MRC output and view the results in UCSF Chimera since it is
a free program.

Q2:
Thanks for your reply. I followed your suggestion and able to visualize the
Channel. But, I am wondering if I could also measure the Channel. Is it
possible by your program?

More specifically, given a structure, can I compute the volume of any
active site using your program? Do you have any other program or webserver
to do that?

A2:
I know the latest subversion source code outputs both the volume and
surface area of the channels. The website shows it as well.

It is up to you to get the parameters right, so that you are only
looking at the channel and not the any extra pockets.

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

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Q:

I am very interested in your recent work "Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells". Could you please advise with respect to the experimental datasets used in your study? I am now looking at the mouse ESC TFs dataset from Chen et al., 2008, provided in their supplemental Table S3. Could you please advise, whether these data refer to the mm8 mouse genome assembly or the mm9 mouse genome assembly? The row data deposited in GEO seem to be updated in 2012, so they are probably re-mapped to mm9. But do you know what was the initial genome build reported in this paper, mm8 or mm9? (For consistency I want to use the "original" peaks reported by Chen et al., and used in your study, not making peak calling again from their row data).

A:
We are pleased to know your interest on the paper. In terms of the Genome assembly, we were using mm8 as the original paper (Chen et al.).

permission for access to libproteingeometry-2.3.1

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Q:

I am interested in using the code of "libproteingeometry-2.3.1" to calculate the molecular surface area for my system (the size is less than 50 atoms). Therefore, I would like to get your explicit permission in order to incorporate the code of "libproteingeometry-2.3.1" into the Gaussian 03 program (commercial program) on the lion clusters of PSU. Thanks a lot!!

A:
That’s fine just make sure you credit via cite and URL. -m

3V online – problem with results download

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Q:

I like your paper about 3V tool and I try to apply it on my proteins. However there seems to be a problem with online version – I cannot get to results through the link provided, e.g. http://geometry.molmovdb.org/3v/tempfiles/nchan8269.pdb.gz

I tried both module for cavities and channels with similar failure.

Could you solve it for me please?

A:
I’ve set up a newer server that provides more feedback at http://3vee.molmovdb.org, I keep the old one around since people still prefer it.

All I can tell from looking at the server is that the file you are looking to download does not exist. So, maybe the program crashed. Try the new site and it might be more informative.

I would try Channel Finder instead of Channel Extraction. Channel Extraction is very particular about finding the exact coordinate of the channel — in fact I may change the algorithm to accommodate for this.